6VEO: ATAD2B bromodomain

ATAD2B bromodomain in complex with 4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione (compound 38). Determined by X-ray diffraction at 2.4 Å resolution. Released 28 Oct 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,284
Mol. weight: 16.53 kDa
Ligands: YD4
Released: 28 Oct 2020

Explore 6VEO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VEO contains 8 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	951-975	25
α-helix	978-983	6
α-helix	986-988	3
α-helix	995-998	4
α-helix	1005-1013	9
α-helix	1020-1037	18
α-helix	1043-1066	24
α-helix	1069-1083	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATPase family AAA domain-containing protein 2B	A	protein	136	Homo sapiens	Q9ULI0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VEO_1 ATPase family AAA domain-containing protein 2B (chains A)
GPLEDQEENTLRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVI
TKIDKHNYLTAKDFLKDIDLICSNALEYNPDKDPGDKIIRHRACTLKDTAHAIIAAELDP
EFNKLCEEIKEARIKR

Ligands and cofactors

ID	Name	Formula	Copies
YD4	4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphth…	C26 H33 N5 O4 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain. Lloyd, J.T., McLaughlin, K., Lubula, M.Y. et al. J Med Chem (2020) 63:12799-12813. DOI 10.1021/acs.jmedchem.0c01178 · PubMed

Other PDB entries of the same protein (UniProt Q9ULI0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8UK5 1.4 Å, Crystal structure of the bromodomain of human ATAD2B in complex with histone H4S1(ph)K5ac
8UHL 1.92 Å, ATAD2B bromodomain in complex with histone H4 acetylated at lysine 12
3LXJ 2.33 Å, Crystal Structure of the Bromodomain of Human AAA domain containing 2B (ATAD2B)
8SDX 2.69 Å, ATAD2B bromodomain in complex with histone H4 acetylated at lysine 5 with Serine 1…
2DKW Solution structure of the bromodomain of human protein KIAA1240

Browse structure collections

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